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The hepatitis B virus – Insights into genetic variability, evolution and Bayesian phylogeographic inference

Ingman, Mikael LU (2018)
Abstract (Swedish)
In terms of genome size, the hepatitis B virus is the smallest virus known to infect humans and its compactness with multiple overlapping reading frames puts restraints on the emergence of mutations. In the papers included in this thesis we aimed to investigate genetic variation within the precore and core promoter region and to describe the origin, spread and diversification of HBV genotype A.

We described a novel insertion in precore causing a frameshift and the abolishment of HBeAg secretion. Through the process of seroconversion viral load decreased by three logs and ALT values normalized concomitantly with the emergence of the mutated variant which could be detected early during the process as a minor variant along with the... (More)
In terms of genome size, the hepatitis B virus is the smallest virus known to infect humans and its compactness with multiple overlapping reading frames puts restraints on the emergence of mutations. In the papers included in this thesis we aimed to investigate genetic variation within the precore and core promoter region and to describe the origin, spread and diversification of HBV genotype A.

We described a novel insertion in precore causing a frameshift and the abolishment of HBeAg secretion. Through the process of seroconversion viral load decreased by three logs and ALT values normalized concomitantly with the emergence of the mutated variant which could be detected early during the process as a minor variant along with the wildtype. The position of the insertion lies within the functionally important encapsidation signal necessary for the packaging of the HBV genome into core particles. Prediction of the structure of the encapsidation signal in the mutant was performed and revealed that functionally important parts of the structure remained intact.

The variability in the core promoter and precore region was described in paper II. Genotypes A-D were studied and mutations were found to occur at key positions as A1762T, G1764A, G1896A and G1899A. The proportions of strains originating in seroconverted patients differed between the four genotypes. A number of rare mutations were found, notably the double mutations C1857T along with G1897A and C1856T together with G1898A.

The evolution, global transmission and expansion of HBV/A has previously been described using a variety of different phylogenetic approaches. The main differences lie in the choice of method for calibrating the molecular clock – the correlation of the observed root-to tip divergence in the tree with units of time. We used a GenBank dataset supplemented with sequence material from the early 70’s and a tip-dating approach with a local clock model that allowed for rate variation between lineages. We showed that the deeper temporal distribution the added sequence material provided was necessary for a statistically robust calculation of tMRCA and evolutionary rate. The main finding in our study indicated a diversification of HBV/A in East Africa/Asia, Europe and West Africa in the 19th century followed by a rapid expansion during the mid-20th century. HBV/A has previously been proposed to have been introduced to Haiti through the trans-Atlantic slave trade, but our study indicated that these strains appear to have been introduced later in an historical contest similar to that describing how HIV was introduced to the Americas.
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author
supervisor
opponent
  • professor Lindh, Magnus, Gothenburg University
organization
publishing date
type
Thesis
publication status
published
subject
keywords
Hepatit B, evolutionsbiologi, fylogeni, Hepatitis B, evolutionary dynamics, Phylogeography
pages
70 pages
publisher
Lund University, Faculty of Medicine
defense location
Rum I1345, BMC I13, Sölvegatan 19 i Lund
defense date
2018-03-09 09:00
ISBN
978-91-7619-583-3
language
English
LU publication?
yes
id
872e725f-0a97-4bb7-8912-42776a1e613b
date added to LUP
2018-03-19 20:49:38
date last changed
2018-11-21 21:38:45
@phdthesis{872e725f-0a97-4bb7-8912-42776a1e613b,
  abstract     = {In terms of genome size, the hepatitis B virus is the smallest virus known to infect humans and its compactness with multiple overlapping reading frames puts restraints on the emergence of mutations. In the papers included in this thesis we aimed to investigate genetic variation within the precore and core promoter region and to describe the origin, spread and diversification of HBV genotype A.<br/> <br/>We described a novel insertion in precore causing a frameshift and the abolishment of HBeAg secretion. Through the process of seroconversion viral load decreased by three logs and ALT values normalized concomitantly with the emergence of the mutated variant which could be detected early during the process as a minor variant along with the wildtype. The position of the insertion lies within the functionally important encapsidation signal necessary for the packaging of the HBV genome into core particles. Prediction of the structure of the encapsidation signal in the mutant was performed and revealed that functionally important parts of the structure remained intact.<br/><br/>The variability in the core promoter and precore region was described in paper II. Genotypes A-D were studied and mutations were found to occur at key positions as A1762T, G1764A, G1896A and G1899A. The proportions of strains originating in seroconverted patients differed between the four genotypes. A number of rare mutations were found, notably the double mutations C1857T along with G1897A and C1856T together with G1898A.<br/><br/>The evolution, global transmission and expansion of HBV/A has previously been described using a variety of different phylogenetic approaches. The main differences lie in the choice of method for calibrating the molecular clock – the correlation of the observed root-to tip divergence in the tree with units of time. We used a GenBank dataset supplemented with sequence material from the early 70’s and a tip-dating approach with a local clock model that allowed for rate variation between lineages. We showed that the deeper temporal distribution the added sequence material provided was necessary for a statistically robust calculation of tMRCA and evolutionary rate. The main finding in our study indicated a diversification of HBV/A in East Africa/Asia, Europe and West Africa in the 19th century followed by a rapid expansion during the mid-20th century. HBV/A has previously been proposed to have been introduced to Haiti through the trans-Atlantic slave trade, but our study indicated that these strains appear to have been introduced later in an historical contest similar to that describing how HIV was introduced to the Americas.<br/>},
  author       = {Ingman, Mikael},
  isbn         = {978-91-7619-583-3},
  keyword      = {Hepatit B,evolutionsbiologi,fylogeni,Hepatitis B,evolutionary dynamics,Phylogeography},
  language     = {eng},
  pages        = {70},
  publisher    = {Lund University, Faculty of Medicine},
  school       = {Lund University},
  title        = {The hepatitis B virus – Insights into genetic variability, evolution and Bayesian phylogeographic inference},
  year         = {2018},
}